Strain identifier

BacDive ID: 7658

Type strain: Yes

Species: Kocuria carniphila

Strain history: CCM 132 <-- J. Arpai 188 ("Micrococcus lactis").

NCBI tax ID(s): 262208 (species)

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General

@ref: 6235

BacDive-ID: 7658

DSM-Number: 16004

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, Gram-positive

description: Kocuria carniphila CCUG 55751 is a microaerophile, Gram-positive bacterium that was isolated from meat.

NCBI tax id

  • NCBI tax id: 262208
  • Matching level: species

strain history

@refhistory
6235<- Z. Pácová, CCM <- L. Kotoucková <- J. Arpai (Micrococcus lactis)
67770CCM 132 <-- J. Arpai 188 ("Micrococcus lactis").

doi: 10.13145/bacdive7658.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Kocuria
  • species: Kocuria carniphila
  • full scientific name: Kocuria carniphila Tvrzová et al. 2005

@ref: 6235

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria carniphila

full scientific name: Kocuria carniphila Tvrzová et al. 2005

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.5
6948094.189positive

colony morphology

@refcolony colormedium used
69276Ivory (1014)ISP 3
69276Lemon yellow (1012)ISP 2
69276Lemon yellow (1012)ISP 6
69276Sulfur yellow (1016)ISP 5
69276Sulfur yellow (1016)ISP 7
69276Zinc yellow (1018)ISP 4
69276Zinc yellow (1018)suter with tyrosine
69276Zinc yellow (1018)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69276noAerial myceliumISP 2
69276noAerial myceliumISP 3
69276noAerial myceliumISP 4
69276noAerial myceliumISP 5
69276noAerial myceliumISP 6
69276noAerial myceliumISP 7
69276noAerial myceliumsuter with tyrosine
69276noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69276noMelanin
69276nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69276DSM_16004_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69276DSM_16004_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69276DSM_16004_image7.jpeg(ISP6, ISP7, SSM+T, SSM-T)Helmholtz-Zentrum für Infektionsforschung GmbH
69276DSM_16004_image8.jpeg(ISP6, ISP7, SSM+T, SSM-T)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 6235
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
6235positivegrowth28
60715positivegrowth37
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 60715
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 99

halophily

  • @ref: 69276
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7.5 %

murein

  • @ref: 6235
  • murein short key: A11.06
  • type: A3alpha L-Lys-L-Ala3

observation

  • @ref: 67770
  • observation: quinones: MK-7(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6927622599arabinose-growth
6927662968cellulose-growth
6927628757fructose+growth
6927617234glucose+growth
6927617268inositol+/-growth
6927637684mannose+growth
6927616634raffinose-growth
6927626546rhamnose-growth
6927617992sucrose+growth
6927618222xylose-growth
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69276+++--++------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69276-+/-+-++/-+/----+/--+-+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6235meatSlovakiaSVKEurope
60715MeatSlovakiaSVKEurope
67770Meat

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Meat

taxonmaps

  • @ref: 69479
  • File name: preview.99_18473.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_424;97_481;98_13945;99_18473&stattab=map
  • Last taxonomy: Kocuria
  • 16S sequence: AM237391
  • Sequence Identity:
  • Total samples: 12186
  • soil counts: 802
  • aquatic counts: 1481
  • animal counts: 9515
  • plant counts: 388

Safety information

risk assessment

  • @ref: 6235
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Kocuria carniphila partial 16S rRNA gene, isolate OS-32.d1AM2373501481nuccore262208
20218Kocuria carniphila partial 16S rRNA gene, isolate OS-32.d2AM2373511418nuccore262208
20218Kocuria carniphila partial 16S rRNA gene, isolate OS-94AM2373791420nuccore262208
20218Kocuria carniphila partial 16S rRNA gene, isolate OS-114AM2373821120nuccore262208
20218Kocuria carniphila partial 16S rRNA gene, isolate OS-130AM2373851420nuccore262208
20218Kocuria carniphila partial 16S rRNA gene, isolate OS-155.bAM2373911419nuccore262208
6235Kocuria carniphila partial 16S rRNA gene, strain CCM 132TAJ6229071515nuccore262208

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kocuria carniphila strain CCM 132262208.3wgspatric262208
66792Kocuria carniphila CCM 1322865693805draftimg262208
67770Kocuria carniphila CCM 132GCA_004136555contigncbi262208

GC content

@refGC-contentmethod
623571
6777071thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno99no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes94.189no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.545no
69480spore-formingspore-formingAbility to form endo- or exosporesno73.488no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.251no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.467no
69480flagellatedmotile2+Ability to perform flagellated movementno93.5no

External links

@ref: 6235

culture collection no.: CCUG 55751, JCM 14118, DSM 16004, CCM 132, NBRC 110786

straininfo link

  • @ref: 77102
  • straininfo: 66427

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653866Reclassification of strain CCM 132, previously classified as Kocuria varians, as Kocuria carniphila sp. nov.Tvrzova L, Schumann P, Sedlacek I, Pacova Z, Sproer C, Verbarg S, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/ijs.0.63304-02005Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Meat/*microbiology, Micrococcaceae/chemistry/*classification/genetics/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny26362332Kocuria subflava sp. nov., isolated from marine sediment from the Indian Ocean.Jiang Z, Zhang WH, Yuan CG, Chen JY, Cao LX, Park DJ, Xiao M, Kim CJ, Li WJAntonie Van Leeuwenhoek10.1007/s10482-015-0587-z2015Aerobiosis, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Indian Ocean, Locomotion, Micrococcaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6235Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16004)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16004
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
60715Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55751)https://www.ccug.se/strain?id=55751
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69276Wink, J.https://cdn.dsmz.de/wink/DSM%2016004.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77102Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID66427.1StrainInfo: A central database for resolving microbial strain identifiers